biotext.org.uk

I’ll also be running an interactive workshop on FuncNet at:

The EMBRACE-ENFIN workshop on Expression, Interactions, and System Level Modeling

Helsinki, 5th-6th October 2009

Couple of upcoming events I’ll be going to…

1. Data Integration in the Life Sciences (DILS 2009) in Manchester next month, with a poster and abstract about FuncNet.

2. EMBL-EBI/ENFIN 2009 annual forum for small-medium enterprises (SMEs), in Vienna in September, with a half-hour talk on the same subject.

No ISMB for me this year, not economically justifiable without a speaking spot.

Andrew.

Update (1-Nov-09): Since writing this post nearly a year ago, I’ve come to realise that I was labouring under quite a few misconceptions myself, about REST. Spotting them all is left as an exercise for the reader. But I’d rather leave it here with this caveat, than remove it and pretend I knew better all along…

Michael Little at Fliquid Studios recently posted an interesting comparison of SOAP vs REST which may have accidentally perpetuated a misconception about SOAP that I believe is fairly common. This post is a response to that and a expanded version of a comment I left on Michael’s site.

The confusion arises from the difference between the communication layer (SOAP) and the databinding layer (aka marshalling/unmarshalling) which is responsible for mediating between language-native data structures and XML. Michael is writing from a PHP point of view, and I’m not sure what PHP SOAP toolkits are like in this regard, but fortunately in the Java world the distinction between the two is made clear, and we have various options for each — although JAX-WS for SOAP and JAXB for databinding are the industry standard specifications.

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One of the current ongoing R&D projects at CATH is the development of a library of web services for both internal and external use. The first step in this process was the selection of a web service toolkit (or ’stack’) to use, as there are several competing (and often mutually incompatible) frameworks available. This page compares some of them in brief based on some informal evaluations and background reading.

Note that I am far from being an expert in this field, so feel free to leave a comment if there’s anything here you disagree with. I am, as ever, happy to be corrected.

Also, please don’t get the impression that this is a methodical side-by-side comparison. I would have liked to implement the exact same non-trivial service in each stack, and report systematically on my experiences with each, but in reality I just didn’t have time to do it that rigourously. What I present here is the result of going through one or two tutorials (mostly of the Hello World/echo-a-string/double-a-number kind), reading the docs, hanging out on forums and garnering opinion from blog posts and articles. And the amount of time I spent with each toolkit is admittedly variable.

I hope it will be useful to someone, despite the caveats.

Andrew.

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